My current non BPG kit had misaligned holes, which is probably what inspired this question.

I ended up plugging and re-drilling, but going from a splayed out Gibson type shape to a tapered PRS shape, the original plugged holes furthest from the nut extend outside the new outline. Luckily my headstock is going to be solid black, so hopefully won't be noticed.

It also inspired me to finally upgrade my plug cutters to an 8 piece set of Forstners & plug cutters. I'll review them in my first build diary.